The instability of rebaudioside A (Reb A) in food product applications during storage challenges their utilization. The pathways of Reb A degradation in aged acidic beverages were investigated. Three Reb A degradation compounds of known sensory importance were monitored, consisting of (1) a rearrangement, (2) a hydration, and (3) an epoxidation/rearrangement product. Using deuterium-labeled water (D2O) experiments, compounds 1–2 were reported to be generated by acid-catalyzed mechanisms involving the formation of a carbocation on carbon position 16, followed by either deprotonation via E1 elimination on C15 to form the more thermodynamically stable trisubstituted alkene (compound 1), or by the Markovnikov addition of water via SN1 substitution to form a tertiary alcohol (compound 2). Compound 3 was generated by epoxidation of the exomethylene at the C16–17 positions, followed by the opening and rearrangement of the ring to form a new alkene bond between C15–C16 and a primary alcohol on C17. Further analysis of the effect of beverage ingredients indicated the addition of caramel color significantly increased (p < 0.0001) the concentrations of compounds 1–2 compared to the aged control by 89 and 83%, respectively, whereas a specific coffee flavor and caramel color were reported to significantly reduce (p < 0.0001) the formation of compound 3 compared to the aged control during storage by 90 and 79%, respectively.